Subtract an array object
I played a bit with this task, creating the basic setup. The screenshots are kinda helpful, but don't tell the full story yet. So in essence, I've created a flat plane with the microstructure on it, and a cylinder wall with the structure on it. Both use the same mesh, all you need to model is this here:

It's a cube with the top face deleted, and then three faces extruded out of that. The cube has the desired 100 um size. Using arrays with the merge option turned on, and the merge tolerance set to something really low like 10 um, you'll get the flat plane with the structure. If you need that with a circular cut around it, you can use one boolean. I didn't do that so far, as I'm not sure where this is going yet.
The sidewall is the same mesh, just one additional modifier added after the arrays: The Bend modifier. I used an Empty to control the direction. And this is what it looks like on the cylinder:

The Blend file is here: 
Based on your own model
Edit Updated Blend file is here: 
As stated in the comment section, I cannot upload the file with modifiers applied, as there is a limit of 30 MB at https://blend-exchange.giantcowfilms.com, and the resulting file is 32MB. By the way, how does blender crash on your end? Because if what you see is Blender freezing for a while, that's just because the modifier calculation takes a long time. On my machine 30 seconds, and this is a real beast. So if that's the case for you, just be patient  :)